Some areas received double the usual September rainfall in 48 hours after tropical storm Etau swept across Japan's main island of Honshu. In some places, rain-swollen rivers burst their banks.

A 63-year old woman was missing in a landslide that hit her home while a man in his 70s in the town of Joso, 56 km (35 miles) north of Tokyo, was feared trapped when water engulfed his home, NHK national television said.

"We heard a huge sound like a thunderclap, and then the hillside came down," a man told NHK, referring to the landslide that swept away his neighbor.

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More than 100,000 flee floods in Japan after 'once-in-50-years' rain

People inside houses wait to be rescued as the houses are submerged in water flooded from a river in Joso, Ibaraki prefecture, northeast of Tokyo Thursday, Sept. 10, 2015. Heavy rain is pummeling Japan for a second straight day, overflowing rivers and causing landslides and localized flooding in the eastern part of the country. (Kyodo News via AP)

A man carries belongings through a flooded street in Oyama, Tochigi prefecture, northeast of Tokyo Thursday, Sept. 10, 2015. Heavy rain is pummeling Japan for a second straight day, overflowing rivers and causing landslides and localized flooding in the eastern part of the country. (Kyodo News via AP)

A person inside a house waves to a helicopter as the house is submerged in water flooded from a river in Joso, Ibaraki prefecture, northeast of Tokyo Thursday, Sept. 10, 2015. Heavy rain is pummeling Japan for a second straight day, overflowing rivers and causing landslides and localized flooding in the eastern part of the country. (Kyodo News via AP)

Rescue workers transport evacuees in a rubber boat through floodwaters at Oyama in Tochigi prefecture, north of Tokyo on September 10, 2015. Authorities in central Japan ordered tens of thousands to flee their homes after torrential rains flooded rivers and triggered landslides, with one person missing after a mudslide buried houses. The Japan Meteorological Agency issued special downpour warnings for Tochigi and Ibaraki prefectures, north of Tokyo, urging vigilance against mudslides and flooding. AFP PHOTO / Yoshikazu TSUNO (Photo credit should read YOSHIKAZU TSUNO/AFP/Getty Images)

People wait for help as the vehicles are submerged in flooding in Joso, Ibaraki prefecture, northeast of Tokyo Thursday, Sept. 10, 2015. Heavy rain is pummeling Japan for a second straight day, overflowing rivers and causing landslides and localized flooding in the eastern part of the country. (Kyodo News via AP)

Members of a local fire brigade stand on a flooded street as they watch a rescue operation by helicopters in Joso city in Ibaraki prefecture, north of Tokyo on September 10, 2015. A Japanese city was flooded when a raging river burst its banks, washing away homes and cars as desperate residents pleaded for help, after tens of thousands were ordered to flee their homes following torrential rains. AFP PHOTO / KAZUHIRO NOGI (Photo credit should read KAZUHIRO NOGI/AFP/Getty Images)

People wait for help as the vehicles are submerged in flooding in Joso, Ibaraki prefecture, northeast of Tokyo Thursday, Sept. 10, 2015. Heavy rain is pummeling Japan for a second straight day, overflowing rivers and causing landslides and localized flooding in the eastern part of the country. (Kyodo News via AP)

Houses are flooded due to heavy rain in Koshigaya, Saitama prefecture, near Tokyo Thursday, Sept. 10, 2015. Heavy rain is pummeling Japan for a second straight day, overflowing rivers and causing landslides and localized flooding in the eastern part of the country. (Kyodo News via AP Photo)

People, sitting on the roof of a car, left, and standing near a utility pole, wait for help in water flooded street in Joso, Ibaraki prefecture, northeast of Tokyo Thursday, Sept. 10, 2015. Heavy rain is pummeling Japan for a second straight day, overflowing rivers and causing landslides and localized flooding in the eastern part of the country. (Kyodo News via AP)

A resident is rescued from a flooded residential area in Joso, Ibaraki prefecture, northeast of Tokyo Thursday, Sept. 10, 2015. Heavy rain is pummeling Japan for a second straight day, overflowing rivers and causing landslides and localized flooding in the eastern part of the country. (Kyodo News via AP)

People are rescued as their vehicles are submerged in flooding in Joso, Ibaraki prefecture, northeast of Tokyo Thursday, Sept. 10, 2015. Heavy rain is pummeling Japan for a second straight day, overflowing rivers and causing landslides and localized flooding in the eastern part of the country. (Kyodo News via AP)

Residents and dogs wait for rescuers as the house is submerged in water flooded from a river in Joso, Ibaraki prefecture, northeast of Tokyo Thursday, Sept. 10, 2015. Heavy rain is pummeling Japan for a second straight day, overflowing rivers and causing landslides and localized flooding in the eastern part of the country. (Kyodo News via AP)

A police helicopter lifts an evacuee with a rescue police officer from floodwaters in Joso city in Ibaraki prefecture, north of Tokyo on September 10, 2015. A Japanese city was flooded when a raging river burst its banks, washing away homes and cars as desperate residents pleaded for help, after tens of thousands were ordered to flee their homes following torrential rains. AFP PHOTO / KAZUHIRO NOGI (Photo credit should read KAZUHIRO NOGI/AFP/Getty Images)

Houses are submerged in water flooded from the Kinugawa River, right bottom, in Joso, Ibaraki prefecture, northeast of Tokyo Thursday, Sept. 10, 2015. As heavy rain pummeled Japan for a second straight day, the river broke through a flood berm, sending a wall of water into Joso, about 50 kilometers (30 miles) northeast of Japan's capital. (Kyodo News via AP)

Local residents wait to be rescued on the roof of their home in a flooded area in Joso, Ibaraki Prefecture, on September 10, 2015. The Japanese city 50 km north east of Tokyo was flooded when Kinugawa river burst its banks, destroying homes and cars as desperate residents waited for help, and as thousands of people were ordered to evacuate. AFP PHOTO/Jiji Press JAPAN OUT (Photo credit should read JIJI PRESS/AFP/Getty Images)

A section of a hotel along a river is collapsed due to heavy rain in Nikko, Tochigi prefecture, north of Tokyo Thursday, Sept. 10, 2015. Heavy rain is pummeling Japan for a second straight day, overflowing rivers and causing landslides and localized flooding in the eastern part of the country. (Kyodo News via AP)

Residents on a rescue boat move through a flooded area in Joso, Ibaraki prefecture, northeast of Tokyo Thursday, Sept. 10, 2015. Heavy rain is pummeling Japan for a second straight day, overflowing rivers and causing landslides and localized flooding in the eastern part of the country. (Kyodo News via AP)

A building of an open-air spa, right, that belongs to Kinugawa Plaza Hotel, falls into the rapid stream of the Kinugawa River swollen by heavy rainfall in Nikko, Tochigi prefecture, northeast of Tokyo Thursday, Sept. 10, 2015. Heavy rain is pummeling Japan for a second straight day, overflowing rivers and causing landslides and localized flooding in the eastern part of the country. (Kyodo News via AP)

Houses are submerged in water flooded from a river in Joso, Ibaraki prefecture, northeast of Tokyo Thursday, Sept. 10, 2015. Heavy rain is pummeling Japan for a second straight day, overflowing rivers and causing landslides and localized flooding in the eastern part of the country. (Kyodo News via AP)

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Television broadcast footage of helicopters winching people to safety, including an elderly couple clutching a pair of struggling dogs as the flood tore away pieces of their home.

A further 800,000 people were at one point advised to evacuate after officials issued predawn warnings of "once in a half century rains" to 5 million people in areas east and north of Tokyo.

Japan has put heavy emphasis on disaster prevention since a 2011 earthquake and tsunami killed nearly 20,000 people and authorities are keen to avoid criticism for what was seen as a sluggish response.

Prime Minister Shinzo Abe warned of more rain and said he was setting up an emergency center.

"The government will work as one to prioritize the safety of the people and do our best to prevent any further disaster," Abe told reporters.

Television footage showed people in Joso waving towels while waiting for help on the upper floors of homes engulfed in floods after the overflowing Kinugawa river swept through.

"I thought I was safe because I live on a hill, but pretty soon the water came up and everything was washed away," a barefoot man told Fuji TV after his helicopter rescue.

Up to 12 military helicopters took part in the rescue along with an initial 55 members of Japan's military, the Self Defence Force. Officials said their number would rise.

Rescue workers rushed to find people before nightfall.

Part of a hotel in the town of Nikko, famed for its shrines and temples, had collapsed, Kyodo news agency said, but there were no reports of injuries.

Rainfall reached 500 mm (20 inches) around Joso, NHK said, with weather officials expecting at least 200 mm (8 inches) more in parts of eastern Japan, including Fukushima, the site of the nuclear reactor crippled in 2011, before the downpour stops on Friday.